Mercurial > repos > iuc > merge_metaphlan_tables

annotate merge_metaphlan_tables.xml @ 1:35c831cdbf7a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 40926b77d62858edbca5b04f73bb0f2aad4da31e"
author iuc
date Fri, 19 Mar 2021 09:39:22 +0000
parents 3b469e230e82
children 3f05bf162005
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3b469e230e82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
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1 <tool id="merge_metaphlan_tables" name="Merge" version="@WRAPPER_VERSION@.0">
3b469e230e82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
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3 <description>MetaPhlAn2 files</description>
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5 <macros>
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6 <import>metaphlan2_macros.xml</import>
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7 </macros>
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3b469e230e82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
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9 <expand macro="requirements"/>
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10 <expand macro="stdio"/>
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12 <version_command>merge_metaphlan_tables.py -v</version_command>
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3b469e230e82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
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14 <command>
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15 <![CDATA[
3b469e230e82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
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16 merge_metaphlan_tables.py
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17 #for $element in $input_files
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18 '$element'
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19 #end for
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20 > '$output'
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21 ]]>
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22 </command>
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24 <inputs>
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25 <param name="input_files" type="data" format="tabular,txt" multiple="True" label="MetaPhlAn2 output file to join" />
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26 </inputs>
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28 <outputs>
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29 <data format="tabular" name="output" label="${tool.name} on ${on_string}: Merged MetaPhlAn2 files" />
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30 </outputs>
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3b469e230e82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
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32 <tests>
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33 <test>
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34 <param name="input_files" value="community_profile.tabular,community_profile.tabular"/>
3b469e230e82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
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35 <output name="output">
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36 <assert_contents>
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37 <has_text text="#SampleID" />
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38 <has_text text="k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_thetaiotaomicron|t__Bacteroides_thetaiotaomicron_unclassified" />
3b469e230e82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
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39 </assert_contents>
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40 </output>
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41 </test>
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42 </tests>
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44 <help><![CDATA[
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46 **What it does**
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3b469e230e82 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
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48 MetaPhlAn is a computational tool to profile the structure and the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data with species level resolution. For more information, check the `user manual <https://bitbucket.org/biobakery/metaphlan2/>`_.
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50 This tool performs a table join on one or more metaphlan output files
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52 ]]></help>
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54 <expand macro="citations"/>
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55 </tool>